Biochemical Systems

and Living Cells

Lecture 3a
Chem 14 – General Biochemistry
LEVELS OF ORGANIZATION OF THE
LIVING ORGANISM

ORGAN
CELL TISSUE ORGANISM
SYSTEMS
Why we need to study organelles of the living cell in
relation to biochemical systems

• Provide information regarding the structure of the cell

and the function and composition of each part.

• Provide understanding of the relation of different

biochemical systems (NUCLEIC ACIDS, PROTEINS,
LIPIDS, CARBOHYDRATES, ENZYMES) to the
organelles of the living cell.
 The Chief Goal of Biochemistry

To understand the

structure and behavior

of biomolecules
 BIOMOLECULES
CARBON-CONTAINING COMPOUNDS that make up the various parts
of the living cell.
They carry out the chemical reactions that enable it to grow,
maintain and reproduce itself, and use and store energy.

https://byjus.com/biology/biomolecules/
 Biomolecules
A vast array of
biomolecules is
present in the cell.
The structure of
each biomolecule
determines in what
chemical reactions it is
able to participate,
and hence what role
it plays in the cell's
life processes.
 CLASSES OF BIOMOLECULES

nucleic acids
lipids

carbohydrates
proteins
 THE CELL THEORY

The most basic similarity is that all living things are

composed of one or more cells.
- This is known as the Cell Theory.
Our knowledge of cells is built on work done with
microscopes.
 Historical Background

• English scientist Robert

Hooke in 1665 first
described cells from his
observations of cork
slices.

• Hooke first used the

word "cell". Drawing of cork under microscope by Robert Hooke
https://www.sciencephoto.com/media/230814/view/drawing-
of-cork-under-microscope-by-robert-hooke
 Historical Background

In 1673, Dutch
amateur scientist
Antoine van
Leeuwenhoek
discovered
microscopic animals
in water.
http://livingthedreamsicle.blogspot.com/2013/09/sep
tember-17-anton-van-leeuwenhoek-and.html
 Historical Background

• German scientists Schleiden and Schwann in

1830's were first to say that all organisms are made
of one or more cells.
• German biologist Virchow in 1858 stated that all
cells come from the division of pre-existing cells.
• Cells are the building blocks of life.
 The Cell Theory
can be summarized as:

1. All living organisms are made up of one or

more cells.
2. The cell is the basic unit of life.
3. All cells come from the division of pre-
existing cells.
Cells come in many shapes and sizes, although most
are microscopic.
Most cells are small, about 0.001 cm in length (1/100 of a
mm, or 10 µm).
The smallest cells of the microorganism mycoplasma
are 0.3 µm in size
Some cells are large.
e.g. some giant algal cells may be several centimeters
long.
A chicken's egg is a single cell.
 Cells come in many shapes and sizes, although most are microscopic.

• 40,000 red blood cells would fill the letter "O" on a page
of type.
• You produce about 2.5 million new red blood cells every
second!
• Each square cm of your skin contains about 150,000 skin
cells.
• Human beings are composed of about 50 to 100 trillion
cells.
Cells carry on all the processes associated
with life, such as reproducing and
interacting with the environment.
https://www.educationobserver.com/forum/attachment.php?aid=34375
 Main Parts of a Cell

Nucleus: specialized structure within

the cell which contains DNA and
controls cell functioning and
reproduction.
Organelles: small bodies with specific
structures and functions within the
cell.
https://www.timvandevall.com/animal-cell-diagram/

Cell Membrane (also Plasma

Cytoplasm: the liquid substance between the
Membrane): the thin layer which
nucleus and the cell membrane, in which the
separates the cell contents from it's
organelles are located.
environment.
Additional Plant Cell Parts
Vacuole: membrane
enclosed, fluid-filled spaces

Plant cells also have a cell

wall surrounding the cell
membrane.

Plastids: membrane-bound
structures that usually
contain pigments and give
plant cells their colors. (i.e.
chloroplast)
A Prokaryotic Cell

The cells of PROKARYOTES

lack a nucleus and other
organelles.

Prokaryotes are unicellular.

 Animal cell
• At the center is the nucleus, which contains the
cell's genetic information.

• The dark ovoid objects spread throughout the

cell are mitochondria, which produce energy
for the cell.

• The small black dots are glycogen granules, the

storage form of glucose.

• Magnification: x8,500 when printed at 10

centimetres tall.
Transmission electron micrograph
(TEM) of a section through a rat liver
cell. https://www.sciencephoto.com/media/493096/view/animal-cell-tem
 Plant Cell
• At the center is the nucleus,
which contains the cell's
genetic information in the
form of DNA
(deoxyribonucleic acid,
black).
• Also within the cell are many
vacuoles (white).

https://www.sciencephoto.com/media/91841
Transmission electron micrograph (TEM) of a sago
8/view/plant-cell-tem
pondweed (Potamogeton pectinatus) cell.
 E. coli O111 bacteria
• These are enterohaemorrhagic E. coli (EHEC), a
dangerous form of the normally benign E. coli
bacteria which live in the intestine.
• Usually transmitted by food poisoning, they can
cause life-threatening diarrhoea, intestinal bleeding,
kidney failure and disturbances to blood clotting.
• There are no effective cures for EHEC, but there are
treatments for dealing with the symptoms of
infection.
• Another strain of EHEC bacteria is E. coli O157:H7.
Magnification: x160,000 at 8x10 inch size.
https://www.sciencephoto.com/media/12555/view/tem-of-escherichia-
Transmission electron micrograph (TEM)
of Escherichia coli O111 bacteria.
coli-0111-bacteria
 The Cell Membrane and the “Fluid Mosaic” Model

Cells are surrounded by a thin membrane of lipid and

protein, about 100 angstroms (100 x 10-10 m) thick.
The CELL MEMBRANE or PLASMA MEBRANE
functions in transport of materials in and out of cell,
recognition, communication, and homeostasis.
It is a remarkable structure that has properties of a solid
and a liquid.
 The Fluid Mosaic Model

It forms a "fluid sea" in which proteins and other

molecules like other lipids or carbohydrates are suspended
(like icebergs) or anchored at various points on its surface.

The “sea” or “fluid” part is composed of side by side

phospholipids arranged in a bilayer (called a lipid
bilayer).
 The Fluid Mosaic Model

The solid part (the “mosaic”) is the variety of proteins and

other molecules embedded in the bilayer.
Each phospholipid has a hydrophobic tail and a
hydrophilic head.
The membrane has consistency of light machine oil.
The membrane is SELECTIVELY PERMEABLE
(will let some substances in but not others of the same
size).
The plasma The Fluid Mosaic Model
membrane that
surrounds
eukaryotic cells is
a dynamic
structure
composed of
two layers of
phospholipid
molecules
interspersed with
cholesterol and
proteins.
Phospholipids
Phospholipids are
composed of a
hydrophilic, or
water-loving,
head and
two tails, which
are hydrophobic,
or water-hating.
 Phospholipids

The two phospholipid layers

face each other in the
membrane, with the heads
directed outward and the
tails pointing inward.
 Phospholipids

The water-attracting heads anchor the membrane to

the cytoplasm, (the watery fluid inside the cell) and
also to the water surrounding the cell.
 Phospholipids

The WATER-HATING TAILS block large

water-soluble molecules from passing through
the membrane while permitting fat-soluble
molecules, including medications such as
tranquilizers and sleeping pills, to freely cross
the membrane.
 Other Biomolecules in Plasma Membrane

Proteins embedded in the

plasma membrane carry
out a variety of
functions, including
transport of large water
soluble molecules such
as sugars and certain
amino acids
 Other Biomolecules in Plasma Membrane

Glycoproteins (proteins bonded

to carbohydrates) serve in part to
identify the cell as belonging to
a unique organism, enabling the
immune system to detect foreign
cells, such as invading bacteria,
which carry different
glycoproteins.
 Other Biomolecules in Plasma Membrane

Cholesterol molecules in the

plasma membrane act as
stabilizers that limit the
movement of the two
slippery phospholipids
layers, which slide back and
forth in the membrane.
 Other Biomolecules in Plasma Membrane

Tiny gaps in the

membrane enable small
molecules such as oxygen
(upper right) to diffuse
readily into and out of the
cell.
 Other Biomolecules in Plasma Membrane

Since cells constantly use up oxygen, its concentration

decreases within the cell. The higher concentration of
oxygen outside the cell causes a net flow of oxygen into
the cell.
The steady stream of oxygen into the cell enables it to
carry out aerobic respiration continually, a process
that provides the cell with the energy needed to carry
out its functions.
 Cell Wall
https://www.timvandevall.com/printables/plant-cell-
diagram-unlabeled-bw/blank-plant-cell-diagram/
Plant Cells have a Cell Wall surrounding
their cell membrane.
The cell wall is made up of a large
number of cellulose fibers cemented
together (like the cellulose fibers in
paper).
Small molecules have little difficulty
penetrating the cell wall, while larger
molecules may not be able to pass
through.
(The cell wall is said to be semi-
permeable.)
 Cell Wall

• Relatively rigid
• Lends shape to plant cell
• Does not participate in cell activity
PLANT CELL WALL is made of
CELLULOSE (long molecule of
carbohydrate).
FUNGI CELL WALL is made of
CHITIN (amino sugar glucosamine).
BACTERIA CELL is made of
MUREIN (polysaccharide chain
https://public.ornl.gov/site/gallery/detail.cfm?id=249
linked by amino acids).
 Chloroplasts & Plastids:
Food Makers for the World
• Found in plant cells only.
• Membrane-bound structures that
usually contain pigments and
give plant cells their colors. The
most prominent plastid is the
CHLOROPLAST.
• Some plastids are storage bodies
for starch, proteins, oils.
 Chloroplasts & Plastids

Cellular structures in plant cells CHROMOPLASTS are colored plastids.

which generally hold pigments
* chloroplasts – chlorophyll bearing
plastids (green color)
* carotenoids/xanthrophylls – yellow or
orange pigments, cream, red and
brown
LEUCOPLASTS are white or colorless
plastids.
* Contains starch, oils, and protein
https://www.qsstudy.com/biology/plastid-definition-
granules
functions
 Chloroplasts & Plastids

Inside the chloroplast are membranous stacks of

grana (look like pancakes) where the chlorophyll
is located.

Each pancake is call a thylakoid.

Chloroplasts are the double-membrane bound organelles in which
PHOTOSYNTHESIS (the conversion of light energy to carbohydrates)
occurs.
The process is basically the opposite of cellular respiration:
CO2 + H2O + ENERGY  Carbohydrate + O2 (i.e. ATP)
Chlorophyll is the chemical that absorbs the energy of the sun to provide the
energy required for reducing CO2 to Glucose.
Vacuoles and Vesicles: Storage Depots
A VESICLE is a small VACUOLE.
• Used for transport and storage of
materials.
Vacuoles and vesicles are formed by:
1) pinching off from the Golgi
apparatus
2) endocytosis of the cell membrane
3) extension of the ER membrane (for
example, the large central vacuole of
a plant cell)
 Vacuoles and Vesicles

Plant cells usually have one large Central

Vacuole.
The plant cell’s central vacuole functions in
1) water storage
2) food storage
3) waste storage
4) cell support

It is thought to be an extension of the ER

membrane.
 Central Vacuole
Membrane enclosed, fluid-filled spaces.
Membrane – TONOPLAST
CELL SAP (fluid) – water with
dissolved substances, such as
salts, sugars and organic acids
FOOD VACUOLES – processing
centers
STORAGE VACUOLES - contains
finished products such as fats
EXCRETORY VACUOLES –
https://micro.magnet.fsu.edu/cells/plants/vacu elimination of wastes
ole.html
PEROXISOMES
PEROXISOMES are single-
membrane organelles.
• Peroxisomal enzymes remove
hydrogen atoms from small
molecules and join the
hydrogen atoms to oxygen to
form hydrogen peroxide, and
then break it down into water
and oxygen.
The Nucleus: the Cell’s CPU

It is the control center or "brain"

of cell.
It contains the DNA and is site
of manufacture of RNA.
A large, centrally located
organelle surrounded by nuclear
envelope.
 The Nucleus

• The nuclear envelope is a

double membrane (2
phospholipid bilayers thick)
that has pores in it for
molecules to enter and
exit).
• The envelope is very
porous and is a continuation
of the membranes of the
endoplasmic reticulum.
https://www.dreamstime.com/illustration/nucleus-cell.html
 The Nucleus

• The pores, called nuclear

pores, allow selected
molecules into and out of
the nucleus.
• It is also believed that these
pores are the routes by
which genetic messages
(RNA) pass into the
cytoplasm.
 The Nucleus

• The DNA is contained by a

number of chromosomes, which
consist of long strands of DNA
tightly wound into coils with
proteins called histones.
• The combination of DNA and
histone proteins is known as
CHROMATIN.
• Chromosomes function in
packaging of DNA during
nuclear division and control of
gene expression
 The Nucleus

LEVELS OF
ORGANIZATION
OF THE
CHROMOSOME

https://www.genome.gov/genetics-glossary/Chromatin
 The Nucleus

• The nucleus, therefore,

determines the metabolism,
growth, differentiation, structure,
and reproduction of cell.

• The nucleus contains one or more

DARK-STAINING discrete
structures, known as
NUCLEOLI, which are sites of
RIBOSOMAL RIBONUCLEIC
ACID (rRNA) SYNTHESIS.
Endoplasmic Reticulum (ER)

The Endoplasmic Reticulum

(ER) is a system of
MEMBRANOUS TUBULAR
CANALS that begins just
outside the nucleus and
branches throughout the
cytoplasm.
 Endoplasmic Reticulum (ER)

• If ribosomes are
attached to the ER, it
is called ROUGH
Endoplasmic
Reticulum.
• The function of rough
ER is protein synthesis.

https://www.pinterest.ph/pin/573505333769252428/
 Endoplasmic Reticulum (ER)

• If no ribosomes are
attached to the ER, it
is called SMOOTH
Endoplasmic
Reticulum.
• The function of
smooth ER is
synthesis of lipids.

https://www.pinterest.ph/pin/573505333769252428/
 Endoplasmic Reticulum (ER)

IMPORTANCE OF LIPIDS
• Required for the growth of the cell membrane and for
the membranes of the organelles within the cell
• Often used to make hormones
• Detoxify drugs and chemicals in the cell (takes place in
peroxisome vesicles which are often attached to
smooth ER)
 Endoplasmic Reticulum (ER)

• The endoplasmic reticulum membranes provide an

increase in surface area where chemical reactions can
occur.

• The channels of the reticulum provide both storage

space for products synthesized by the cell and
transportation routes through which material can travel
through other parts of the cell.
 Endoplasmic Reticulum (ER)

• The endoplasmic reticulum is also the cell's membrane

factory.

• Phospholipids and cholesterol, the main components of

membranes throughout the cell, are synthesized in the
smooth ER.
 Endoplasmic Reticulum (ER)

• Most of the proteins leaving the endoplasmic

reticulum are still not mature.
• They must undergo further processing in another
organelle, the Golgi apparatus, before they are
ready to perform their functions within or
outside the cell.
Ribosomes

• Ribosomes consist of rRNA and

proteins.

• rRNA is produced in the nucleolus

and joined with proteins -- then
migrate through the nuclear pore to
the cytoplasm for final assembly.

• Ribosomes attach themselves to the

endoplasmic reticulum.
 Ribosomes

• Each ribosome is made of 2

non-identical subunits: the
LARGE and SMALL
SUBUNITS.
• It functions as the site for
PROTEIN SYNTHESIS.

https://www.microscopemaster.com/ribosomes.html
Golgi Apparatus
• Golgi Apparatus is a stack of flattened,
hollow cavities enclosed by
membranes, which is often continuous
with the membranes of the endoplasmic
reticulum.
• The organelle is also called the Golgi
complex or Golgi body.
• Located near to the nucleus and ER.
• Named after an Italian anatomist of the
nineteenth century, Camillo Golgi.
 Golgi Apparatus

• The stack is made of a half-

dozen or more saccuoles and
looks like a flattened stack of
hollow tubes.
• Each sac in the organelle
contains enzymes that modify
proteins as they pass through.
• The Golgi apparatus functions
in modification, assembly,
packaging, storage and
secretion of substances.
 Golgi Apparatus

• The Golgi Apparatus receives newly

manufactured protein (from the ER)
on its inner surface.
• Within the Golgi apparatus, the
proteins are sorted out, labeled, and
packaged into vesicles that "pinch
off” the outer surface of the
saccuoles.
• These vesicles can then be
transported to where they are needed
within the cell, or can move to the
cell membrane for export to the
outside of the cell by exocytosis.
Lysosomes: Cellular “Stomachs”

• Special vesicles which are

formed by the Golgi
apparatus.

• They contain powerful

hydrolytic enzymes
 Lysosomes

Functions in

1) cellular digestion

2) autodigestion or disposal of
damaged cell components like
mitochondria

3) breakdown of a whole cell (by

releasing their contents into the
cell cytoplasm)

https://www.dreamstime.com/anatomy-lysosome-hydrolytic- For this reason, they are sometimes

enzymes-membrane-transport-proteins-organelle-use-enzymes-to-
break-down-digest-image124945113 called “suicide sacs.”
 Lysosomes

Lysosomes are known to contain over 40

different enzymes that can digest almost
anything in the cell, including proteins, RNA,
DNA, and carbohydrates.
 Lysosomes

Lysosomes also appear to perform other

digestive processes, such as those connected
with phagocytosis and pinocytosis.
Lysosomes help destroy invading bacteria.
 Mitochondria:
the Cell’s Powerhouse

Mitochondria are the largest

organelles in an animal cell,
after the nucleus.
Are sausage-shaped or
filamentous structures
surrounded by a double-
layered membrane.
 Mitochondria

Mitochondria vary in diameter

from 0.5 to 1 micrometer and in
length up to 7 micrometers.
(about the size of bacteria).

The mitochondrion has two

membranes: outer and inner.
https://biologydictionary.net/mitochondria/

The inner is convoluted into shelf-like folds called cristae.

The enzymes responsible for cellular respiration are arranged, in
assembly-line fashion, on the cristae. This is where energy is produced.
 Mitochondria

• A mitochondrion functions in AEROBIC ENERGY

METABOLISM (also called CELLULAR
RESPIRATION).
• It converts glucose and fatty acids to ATP, the cell's
primary energy molecule, as well as lesser amounts
of other energy rich molecules.
 Mitochondria

The overall formula for cellular respiration is:

Carbohydrate + O2  CO2 + H2O + ENERGY (i.e. ATP)

In the end, 38 molecules of ATP (adenosine

triphosphate) are formed for every molecule of sugar
that is used up in respiration.
 Mitochondria

• Besides supplying energy, mitochondria also help

control the concentration of water, calcium, and other
charged particles (ions) in the cytoplasm.
• Mitochondria have some of their own DNA molecules
and ribosomes that resemble those of prokaryotic cells.
• Human mitochondrial DNA is a closed, circular
molecule 16,569 nucleotide pairs long.
 Mitochondria

• Mitochondria are also self-replicating. They

"reproduce" by splitting in half.
• Mitochondria may have evolved from bacteria that
once developed a close relationship with primitive
eucaryotic cells, and then lost the capacity to live
outside the cell.
 Mitochondria

Another interesting characteristic of human

mitochondria is the fact that all of a person's
mitochondria are descendants of those of his
or her mother.
PROKARYOTIC VS. EUKARYOTIC CELLS

Two classes of cells exist:

 PROKARYOTES
 EUKARYOTES
 PROKARYOTIC VS. EUKARYOTIC CELLS

• The PROKARYOTES include the bacteria and the

blue-green algae (the Monera kingdom).
• These are all single-celled organisms that lack both
a true nucleus and other membrane-bounded
cellular substructures.
• Prokaryotic DNA is usually circular.
 PROKARYOTIC VS. EUKARYOTIC CELLS

• The Eukaryotes include plants, animals, protozoa,

and fungi.
• These cells contain nuclei and other membrane-
bound organelles. The genetic material is organized
into chromosomes.
Eukaryotic Structure Prokaryotic Animal Plant
Cell Membrane YES YES YES
Cell Wall YES NO YES
Nucleus NO YES YES
Mitochondria NO YES YES
Chloroplasts NO NO YES
ER NO YES YES
Ribosomes YES, (small) YES, large YES, large
Vacuoles NO YES, small YES
Lysosomes NO YES, usually NO, usually
Cytoskeleton NO YES YES
Centrioles NO YES NO
References
Ahern, K. Rajagopal, I. and Tan, T. (2018). Biochemistry Free
For All. Creative Commons, Non-commercial use.
https://biochem.oregonstate.edu/sites/biochem.oregonstate.edu/fil
es/ahern/Biochemistry
Raycroft. Biology 12 - Cell Structure & Function: Chapter Notes.
https://www.educationobserver.com/forum/attachment.php?aid=3
4375
Analytical Techniques in Aquaculture Research.
https://aquaculture.ugent.be/Education/coursematerial/online%20
courses/ATA/analysis/lip_phos.htm